Using multiple softwares for performing a simulation

Discussion about building and installing Elmer
annier
Posts: 1141
Joined: 27 Aug 2013, 13:51
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Re: Using multiple softwares for performing a simulation

Post by annier »

Lecture notes on Continuum Mechanics, Fracture Mechanics and FEM
1. Continuum Mechanics
2. Fracture Mechanics
3. Finite Element Method

Integrating DFT and MD for snap potentials
1. Tutorials on Quantum Espresso software
2. Tutorials on the LAMMPS software
3. Professor Boris Kozinsky and Materials Intelligence Research group
(a) Tutorials in LAMMPS and molecular dynamics
(b) Tutorials in DFT theory (first principle energy methods) and Quantum Espresso
(c) Tutorials in DFT theory (materials properties from DFT) and Quantum Espresso
4. TopoTools for visualizing molecular dynamics simulations
5. ATOMSK - a computer tool for dealing with atomic data during MD and DFT calculations
6. VMD software
7. WOLVERTON research group in materials science
8. OVITO software
9. ATOMEYE software


Ubuntu -desktop and WSL system
1. https://askubuntu.com/questions/1162808 ... -18-04-lts
2. https://askubuntu.com/questions/993225/ ... as-of-2018

Tutorials on Support Vector Machine (SVM)
1. Explanatory tutorial
2. scikit-learn website

polynomial regression and genomic datascience using python tools
1. Curve and surface fitting in python
2. statsmodels-statistics in python
3. multivariate polynomial regression or supervised machine learning example
4. Multiple linear regression or supervised machine learning using python
5. Definitions of robustness and accuracy of data analysis using multivariate regression
6. Deep learning for small datasets
7. Metrics-Receiver operating characteristics curve and Area under curve
8. Understanding the format of genomic data
9. Sequence formats-genomatics website
10. Example of svm with tensorflow and keras

Converting latex equations to words using html mathjax format
1. Example
2. Steps

Dataset and scientific queries related ... ealthcare)
1. Introduction

2. CORD-19 dataset

FEM framework for proteins simulations
1. Pymol and surface solvent
2. Pymol software for beginners
3. FFEA - Fluctuating Finite Element Analysis
4. FFEA at bitbucket repository
5. GAMer - software for Geometry and meshing tool for proteins simulations using FEA
6. Fenics software
7. FOLDING@HOME - virtual supercomputers for protein simulations
8. threevis library
4. openmesh-python library


Literatures on Spikes-ACE2 interaction
1. Role of ACE2 in COVID-19
Last edited by annier on 07 Apr 2020, 02:53, edited 1 time in total.
Anil Kunwar
Department of Materials Engineering, KU Leuven, Belgium
annier
Posts: 1141
Joined: 27 Aug 2013, 13:51
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Re: Using multiple softwares for performing a simulation

Post by annier »

Geometry and mesh for structural biology
In order to perform finite element simulations with biological molecules, including proteins, it is necessary to preserve the geometry of the actual molecular structure. pygamer is one of the softwares capable for building geometry/mesh of molecular structures.
For many computers, the pip install command works for installing this software in Ubuntu OS as follow:

Code: Select all

$ pip install pygamer
In some computers, where project cannot install via wheels , as mentioned in https://discuss.python.org/t/pep-517-an ... wheels/791, the website of pygamer software offers an alternative using setuptools and cmake . The build and install via setup tools, as performed in Ubuntu 16.04 computer with python3 is provided as following:

Requirements: python version 3.6 or above

1. Installation method for pygamer software using setuptools in Ubuntu 16.04
a. Install scikit-build using pip

Code: Select all

$ python -m pip install scikit-build
2. Build and install pygamer in accordance to the following commands given in the website of the software

Code: Select all

$ python setup.py build 

Code: Select all

$ python setup.py install
References:
1. Lee et al, Biophysical Journal , 118 (2020), 1003-1008
2. https://www.biorxiv.org/content/10.1101/534479v1
Anil Kunwar
Department of Materials Engineering, KU Leuven, Belgium
annier
Posts: 1141
Joined: 27 Aug 2013, 13:51
Antispam: Yes

Re: Using multiple softwares for performing a simulation

Post by annier »

ipynb to py converter or vice versa
Reference: https://pypi.org/project/ipynb-py-convert/
1. Install ipynb-py-convert using conda installation '

Code: Select all

$ conda install -c defaults -c conda-forge ipynb-py-convert
2. Convert .py to ipynb or vice versa using the following commands
(a) .py to .ipynb

Code: Select all

$ipynb-py-convert abcd.py abcd.ipynb
(b) .ipynb to .py

Code: Select all

$ipynb-py-convert  abcd.ipynb abcd.py

Multi-label and multi-output classification in tensorflow keras
1.https://sanjayasubedi.com.np/deeplearni ... put-keras/
2. https://link.springer.com/article/10.10 ... 010-0483-4
3. https://www.tensorflow.org/guide/keras/rnn
4. https://towardsdatascience.com/multi-la ... c1ab1afede
5. https://towardsdatascience.com/categori ... 1ef77fb5bd
6. https://machinelearningmastery.com/mult ... g-library/
7. https://machinelearningmastery.com/bina ... g-library/
8. https://www.tensorflow.org/tutorials/ke ... sification
9. https://www.pluralsight.com/guides/classification-keras
10. https://medium.com/datadriveninvestor/b ... 3656c726c1
11. https://towardsdatascience.com/classify ... 3101fe0f98
12. https://www.bmc.com/blogs/keras-neural- ... ification/
13. https://towardsdatascience.com/building ... c8abbc17f5

Weights (wi) and biases(bi) in neural network models
1. extracting wi and bi in tensorflow
2. getting weight and bias using keras frontend
3. examples of layer.get_weights()
4. Illustration between prediction output and weights

Notes on machine learning
1. machinecurve website by Chris
2. github repositories containing computer codes associated with machinecurve website
3. https://ml-cheatsheet.readthedocs.io/en ... ation.html
4. Theory of convolution neural network - (I)
5. Theory of convolution neural network -(II)
6. Discussion on the architecture of weights and biases in a neural network
7. Notes on Convolution Neural Network

Discussion on accuracy of neural network model

COVID-19 dataset and machine learning

News on scientific applications of AI and machine learning


Illustrative tutorial for coding using git
Hyperparameters of the neural network

http://www.rin.ac.uk/system/files/attac ... idance.pdf
Last edited by annier on 05 Jul 2020, 10:44, edited 6 times in total.
Anil Kunwar
Department of Materials Engineering, KU Leuven, Belgium
annier
Posts: 1141
Joined: 27 Aug 2013, 13:51
Antispam: Yes

Re: Using multiple softwares for performing a simulation

Post by annier »

Learning rate and optimizer in neural network
1. https://www.tensorflow.org/api_docs/pyt ... izers/Adam
2. https://www.programcreek.com/python/exa ... izers.Adam
3. https://faroit.com/keras-docs/0.2.0/optimizers/
4. https://stackoverflow.com/questions/597 ... rning-rate
5. https://www.kaggle.com/residentmario/keras-optimizers
6. https://www.machinecurve.com/index.php/ ... ange-test/
7. https://www.jeremyjordan.me/nn-learning-rate/
8. https://keras.io/api/optimizers/
9. https://github.com/tensorflow/tensorflow/issues/23728
10. https://keras.io/api/optimizers/adam/
11. https://machinelearningmastery.com/unde ... -networks/
12. https://www.pyimagesearch.com/2019/07/2 ... and-decay/
13. https://www.pyimagesearch.com/2019/10/2 ... rflow-2-0/
14. https://towardsdatascience.com/the-actu ... 4b49f07ea3
15. https://towardsdatascience.com/optimizi ... 2ed38c8345
16. https://ladvien.com/lego-deep-learning-classifier-cnn/
17. https://www.dlology.com/blog/quick-note ... -in-keras/
18. https://www.avanwyk.com/finding-a-learn ... sorflow-2/
19. https://www.machinecurve.com/index.php/ ... ith-keras/
20. https://keras.io/api/callbacks/tensorboard/
21. https://stackoverflow.com/questions/481 ... 9#48206009
22. https://stackoverflow.com/questions/540 ... -optimizer
23. http://sujitpal.blogspot.com/2019/06/un ... yclic.html
24. https://colab.research.google.com/drive ... bBe7n3y3oQ

25. https://www.pyimagesearch.com/2019/08/0 ... te-finder/

Recurrent Neural Network and LSTM
1. Andrej Karpathy's explanation about RNN and its great effectiveness

The Materials Simulation Toolkit for Machine Learning (MAST-ML)
1. https://www.sciencedirect.com/science/a ... 5620300355
2. https://mastmldocs.readthedocs.io/en/latest/index.html

Tutorials on image classification
1. user data reading in tensorflow model
2. cnn using tensorflow and keras
3. Use of the tensorboard
4. Optimization of machine learning models
5. model prediction
6. Notes on convolutional neural network
7. pymks website
8. Conda installation of scikit-learn 0.18 version for importing RandomizedPCA module
9. Installation of updated version of scikit-learn using conda
10. Example on the use of morphological gradient operator using python opencv library

Literatures in batch normalization in activation layers of neural networks
1. theory
2. explanation of backpropagation and batch normalization in feed forward neural network
3. Batch normalization in tf.keras
4. Batch normalization in 3D convolution neural networks
5. Using batch normalization in tensorflow

Climate Science
1. Temperature and rainfall data of different weather stations in Nepal
2.Another dataset for weather data in Nepal

julia programming language in ubuntu
1. Installation of julia in Ubuntu
2. https://docs.julialang.org/en/v1/manual ... fferences/
3. https://docs.julialang.org/en/v1/
4. https://julialang.org/downloads/platfor ... nd_freebsd
5. https://juliaacademy.com/courses
6. https://juliaacademy.com/courses

Arrow setup in GIMP software
(i.) https://graphicdesign.stackexchange.com ... -gimp-2-10
(ii) arrow setup in gimp in linux operating system

Mathematical approximations of x*ln(x)
Anil Kunwar
Department of Materials Engineering, KU Leuven, Belgium
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